{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001525","ANALYSIS_ID":"AN002546","VERSION":"1","CREATED_ON":"November 11, 2020, 2:10 pm"},

"PROJECT":{"PROJECT_TITLE":"Perfluorooctanesulfonic acid (PFOS) and perfluorohexanesulfonic acid (PFHxS) alter the blood lipidome and the hepatic proteome in a murine model of diet-induced obesity","PROJECT_TYPE":"Lipidomics","PROJECT_SUMMARY":"Perfluorooctanesulfonic acid (PFOS) and perfluorohexanesulfonic acid (PFHxS) alter the blood lipidome and the hepatic proteome in a murine model of diet-induced obesity","INSTITUTE":"University of Rhode Island;University of Georgia","DEPARTMENT":"Pharmaceutical and Biomedical Sciences","LABORATORY":"Cummings/Slitt","LAST_NAME":"Ingram;Cummings","FIRST_NAME":"Lishann;Brian","ADDRESS":"250 West Green Street","EMAIL":"ingram@carnegiescience.edu;briansc@uga.edu","PHONE":"706-542-3792","FUNDING_SOURCE":"NIEHS;DOD"},

"STUDY":{"STUDY_TITLE":"Perfluorooctanesulfonic acid (PFOS) and perfluorohexanesulfonic acid (PFHxS) alter the blood lipidome and the hepatic proteome in a murine model of diet-induced obesity","STUDY_SUMMARY":"Perfluorooctanesulfonic acid (PFOS) and perfluorohexanesulfonic acid (PFHxS) alter the blood lipidome and the hepatic proteome in a murine model of diet-induced obesity","INSTITUTE":"University of Rhode Island;University of Georgia","DEPARTMENT":"Pharmaceutical and Biomedical Sciences","LABORATORY":"Cummings/Slitt","LAST_NAME":"Ingram","FIRST_NAME":"Lishann","ADDRESS":"250 West Green Street Athens, GA 30605","EMAIL":"ingram@carnegiescience.edu","PHONE":"706-542-3792"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6","AGE_OR_AGE_RANGE":"8 weeks","GENDER":"Male and female","ANIMAL_ANIMAL_SUPPLIER":"Jackson Labs (Bar Harbor, ME USA)"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"S1",
"Factors":{"Diet":"LFD","Treatment":"none"},
"Additional sample data":{"RAW_FILE_NAME":"rf1"}
},
{
"Subject ID":"-",
"Sample ID":"S2",
"Factors":{"Diet":"LFD","Treatment":"none"},
"Additional sample data":{"RAW_FILE_NAME":"rf2"}
},
{
"Subject ID":"-",
"Sample ID":"S3",
"Factors":{"Diet":"LFD","Treatment":"none"},
"Additional sample data":{"RAW_FILE_NAME":"rf3"}
},
{
"Subject ID":"-",
"Sample ID":"S4",
"Factors":{"Diet":"LFD","Treatment":"none"},
"Additional sample data":{"RAW_FILE_NAME":"rf4"}
},
{
"Subject ID":"-",
"Sample ID":"S5",
"Factors":{"Diet":"LFD","Treatment":"none"},
"Additional sample data":{"RAW_FILE_NAME":"rf5"}
},
{
"Subject ID":"-",
"Sample ID":"S6",
"Factors":{"Diet":"LFD","Treatment":"none"},
"Additional sample data":{"RAW_FILE_NAME":"rf6"}
},
{
"Subject ID":"-",
"Sample ID":"S7",
"Factors":{"Diet":"LFD","Treatment":"PFOS"},
"Additional sample data":{"RAW_FILE_NAME":"rf7"}
},
{
"Subject ID":"-",
"Sample ID":"S8",
"Factors":{"Diet":"LFD","Treatment":"PFOS"},
"Additional sample data":{"RAW_FILE_NAME":"rf8"}
},
{
"Subject ID":"-",
"Sample ID":"S9",
"Factors":{"Diet":"LFD","Treatment":"PFOS"},
"Additional sample data":{"RAW_FILE_NAME":"rf9"}
},
{
"Subject ID":"-",
"Sample ID":"S10",
"Factors":{"Diet":"LFD","Treatment":"PFOS"},
"Additional sample data":{"RAW_FILE_NAME":"rf10"}
},
{
"Subject ID":"-",
"Sample ID":"S11",
"Factors":{"Diet":"LFD","Treatment":"PFOS"},
"Additional sample data":{"RAW_FILE_NAME":"rf11"}
},
{
"Subject ID":"-",
"Sample ID":"S12",
"Factors":{"Diet":"LFD","Treatment":"PFOS"},
"Additional sample data":{"RAW_FILE_NAME":"rf12"}
},
{
"Subject ID":"-",
"Sample ID":"S13",
"Factors":{"Diet":"LFD","Treatment":"PFHxS"},
"Additional sample data":{"RAW_FILE_NAME":"rf13"}
},
{
"Subject ID":"-",
"Sample ID":"S14",
"Factors":{"Diet":"LFD","Treatment":"PFHxS"},
"Additional sample data":{"RAW_FILE_NAME":"rf14"}
},
{
"Subject ID":"-",
"Sample ID":"S15",
"Factors":{"Diet":"LFD","Treatment":"PFHxS"},
"Additional sample data":{"RAW_FILE_NAME":"rf15"}
},
{
"Subject ID":"-",
"Sample ID":"S16",
"Factors":{"Diet":"LFD","Treatment":"PFHxS"},
"Additional sample data":{"RAW_FILE_NAME":"rf16"}
},
{
"Subject ID":"-",
"Sample ID":"S17",
"Factors":{"Diet":"LFD","Treatment":"PFHxS"},
"Additional sample data":{"RAW_FILE_NAME":"rf17"}
},
{
"Subject ID":"-",
"Sample ID":"S18",
"Factors":{"Diet":"LFD","Treatment":"PFHxS"},
"Additional sample data":{"RAW_FILE_NAME":"rf18"}
},
{
"Subject ID":"-",
"Sample ID":"S19",
"Factors":{"Diet":"HFD","Treatment":"none"},
"Additional sample data":{"RAW_FILE_NAME":"rf19"}
},
{
"Subject ID":"-",
"Sample ID":"S20",
"Factors":{"Diet":"HFD","Treatment":"none"},
"Additional sample data":{"RAW_FILE_NAME":"rf20"}
},
{
"Subject ID":"-",
"Sample ID":"S21",
"Factors":{"Diet":"HFD","Treatment":"none"},
"Additional sample data":{"RAW_FILE_NAME":"rf21"}
},
{
"Subject ID":"-",
"Sample ID":"S22",
"Factors":{"Diet":"HFD","Treatment":"none"},
"Additional sample data":{"RAW_FILE_NAME":"rf22"}
},
{
"Subject ID":"-",
"Sample ID":"S23",
"Factors":{"Diet":"HFD","Treatment":"none"},
"Additional sample data":{"RAW_FILE_NAME":"rf23"}
},
{
"Subject ID":"-",
"Sample ID":"S24",
"Factors":{"Diet":"HFD","Treatment":"none"},
"Additional sample data":{"RAW_FILE_NAME":"rf24"}
},
{
"Subject ID":"-",
"Sample ID":"S25",
"Factors":{"Diet":"HFD","Treatment":"PFOS"},
"Additional sample data":{"RAW_FILE_NAME":"rf25"}
},
{
"Subject ID":"-",
"Sample ID":"S26",
"Factors":{"Diet":"HFD","Treatment":"PFOS"},
"Additional sample data":{"RAW_FILE_NAME":"rf26"}
},
{
"Subject ID":"-",
"Sample ID":"S27",
"Factors":{"Diet":"HFD","Treatment":"PFOS"},
"Additional sample data":{"RAW_FILE_NAME":"rf27"}
},
{
"Subject ID":"-",
"Sample ID":"S28",
"Factors":{"Diet":"HFD","Treatment":"PFOS"},
"Additional sample data":{"RAW_FILE_NAME":"rf28"}
},
{
"Subject ID":"-",
"Sample ID":"S29",
"Factors":{"Diet":"HFD","Treatment":"PFOS"},
"Additional sample data":{"RAW_FILE_NAME":"rf29"}
},
{
"Subject ID":"-",
"Sample ID":"S30",
"Factors":{"Diet":"HFD","Treatment":"PFOS"},
"Additional sample data":{"RAW_FILE_NAME":"rf30"}
},
{
"Subject ID":"-",
"Sample ID":"S31",
"Factors":{"Diet":"HFD","Treatment":"PFHxS"},
"Additional sample data":{"RAW_FILE_NAME":"rf31"}
},
{
"Subject ID":"-",
"Sample ID":"S32",
"Factors":{"Diet":"HFD","Treatment":"PFHxS"},
"Additional sample data":{"RAW_FILE_NAME":"rf32"}
},
{
"Subject ID":"-",
"Sample ID":"S33",
"Factors":{"Diet":"HFD","Treatment":"PFHxS"},
"Additional sample data":{"RAW_FILE_NAME":"rf33"}
},
{
"Subject ID":"-",
"Sample ID":"S34",
"Factors":{"Diet":"HFD","Treatment":"PFHxS"},
"Additional sample data":{"RAW_FILE_NAME":"rf34"}
},
{
"Subject ID":"-",
"Sample ID":"S35",
"Factors":{"Diet":"HFD","Treatment":"PFHxS"},
"Additional sample data":{"RAW_FILE_NAME":"rf35"}
},
{
"Subject ID":"-",
"Sample ID":"S36",
"Factors":{"Diet":"HFD","Treatment":"PFHxS"},
"Additional sample data":{"RAW_FILE_NAME":"rf36"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"The study investigated diet-PFAS interactions and the impact of perfluorooctanesulfonic acid (PFOS) and perfluorohexanesulfonic (PFHxS) on the hepatic proteome and blood lipidomic profiles. The results supported the hypothesis that PFOS and PFHxS increase the risk of metabolic and inflammatory disease induced by diet.","SAMPLE_TYPE":"Blood (whole)","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"The mice were fed either a 10.5% kcal, low fat diet (LFD) (D12328, Research Diets, New Brunswick), or a 58% kcal, high fat diet (HFD) (D12331, Research Diets, New Brunswick). The mice were assigned to either diet alone, as controls, or to diet containing 0.0003% PFOS or 0.0003% PFHxS. The resulting treatment groups were as follows: low fat diet (LFD), high fat high carbohydrate diet (HFHC), LFD + PFOS (LPFNA), HFHC + PFOS (HPFOS), LFD + PFHxS (LPFHxS), and HFHC + PFHxS (HPFHxS) at n = 6 per treatment group."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Blood lipids were isolated for lipidomic analysis according to the Bligh and Dyer method (Bligh and Dyer 1959). The lipidomics was performed at the University of Georgia (Athens, GA). Briefly, blood samples designated for lipidomics were suspended in 1.25 ml of methanol and 1.25 ml of chloroform. Tubes were vortexed for 30 s, allowed to sit for 10 min on ice, centrifuged (300 x g; 5 min), and the bottom chloroform layer was transferred to a new test tube. The extraction steps were repeated three times and the chloroform layer combined. A commercial mix of SPLASH Lipidomix internal standards (Avanti Polar Lipids, Inc.) were spiked into each sample. SPLASH Lipidomix Mass Spec standards includes all major lipid classes at ratios similar to that found in human plasma. The collected chloroform layers were dried under nitrogen, reconstituted with 50 µl of methanol: chloroform (3:1 v/v), and stored at 80ºC until analysis. Lipid content was quantified by determining the level of inorganic phosphorus using the Bartlett Assay (Bartlett 1959)."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo-Fisher LTQ Orbitrap Elite","COLUMN_NAME":"Bruker Micron Magic nanoC18 (130mm X 100 µm, 5 µm)","FLOW_RATE":"450-500 nL/min","SOLVENT_A":"0.1% formic acid/water","SOLVENT_B":"mobile phase B was 0.1% formic acid/acetonitrile","INJECTION_TEMPERATURE":"7 °C","TIME_PROGRAM":"60 mins","TARGET_SAMPLE_TEMPERATURE":"7 °C","CHROMATOGRAPHY_COMMENTS":"nanoC18 column (length, 130 mm; i.d., 100 μm; particle size, 5 μm; pore size, 150 Å; max flow rate, 500 nL/min; packing material, Bruker Micron Magic 18)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Lipid structures were identified based on the retention time and subsequent MS/MS spectra. Essentially, we determined structural information through LC-MS/MS and normalization of available lipid standards using LipidMatch. First, lipidomics data processed lipid features using MZmine as described in (Koelmel et al. 2017). Features observed in the blanks were removed using the blank feature filtration method (Patterson et al. 2017). The blank feature filtration method compared to various other filtering methods has been shown to increase the removal of true negatives while decreasing the removal of true positives (Patterson et al. 2017). The resulting MZmine features were annotated using LipidMatch (Koelmel et al. 2017). These annotations are putative, as annotations are based on in-silico MS/MS spectral libraries without matching internal standards for validation and without confirmation using orthogonal approaches (Sumner et al. 2007). The lipid match program then provided a single point calibration using exogenous lipid internal calibrant that best represents the lipid feature (based on lipid class, adduct and retention time). An R script was applied that combined multiple lipid features (adducts) into one feature 4 representing a unique lipid molecule. All open source lipidomics tools are published and available at http://secim.ufl.edu/ secim-tools/.","MS_RESULTS_FILE":"ST001525_AN002546_Results.txt UNITS:unknown Has m/z:Yes Has RT:Yes RT units:Minutes"}

}